OE IRC 8Feb07

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5:25 PM

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hjd_mgi: Avast maties!

jrichter: Hello, folks.

jclark: Hi

Alex_MGI: Been ages, it seems!

jclark: true

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5:30 PM

midori: OK, it's 5:30. Let the fun begin!

jrichter: Hooray!

midori: Do you have any topics?

jrichter: I'd like to say a quick thing about what I've been doing, and what I will be doing this month. Otherwise, I've got nothing beyond your agenda topics.

midori: OK, go ahead.

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jrichter: Because of some funding weirdness in our group, this month I am funded by NCBO, not GO.

jrichter: This has to do with the grant renewal and the way LBL releases funds.

midori 's head starts to spin ...

jrichter: Anyway, because of this, I've been working with Phenote this month, and I will be the entire rest of the month.

jrichter: The good news is that Phenote is built on top of the OBO-Edit sources, so I'm still really working on OBO-Edit 2.0

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midori: Ah ... that's highly relevant to one of the topics I thought up, namely the 1.1release prognosis.

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5:35 PM

jrichter: I may have some time to do OBO-Edit 1.1 development too. I just can't focus on it 100%.

jrichter: What I've been doing for Phenote will be really useful for us, though. Mark needs the reasoner to have a much smaller memory footprint, and I've gotten some good initial results when I started putting the reasoner data in a SQL database.

jrichter: Anyway, that's all I wanted to say on that topic.

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midori: Stuff about the reasoner sounds good.

MelissaH: Hi there.

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MelissaH: sorry I am late.

midori: Given that you can't work as much on 1.1, can you guesstimate how long before we might be able to release it? (Not trying to crack the whip here; just looking to stay informed.)

tberardi: What

tberardi: (sorry)

Alex_MGI: I'm getting concerned that the 1.1 release is taking a long time, but I guess that can't be helped too much this month.

jrichter: It's hard to say. I can probably clean up all the (real) outstanding tracker bugs in about 3 days, but there's also documentation and turnaround time...

jrichter: ...for testing.

jrichter: Hmmm....

jrichter: How about this?

5:40 PM

jrichter: What if I work on OBO-Edit bug fixes Monday - Wednesday of next week. There will be a new beta release on Thursday, even if I haven't gotten through all the bug reports. That way we can at least make some headway.

midori: OK by me ...

Alex_MGI: Good.

jrichter: Anything else on that topic, then?

jclark: has there been much targeted testing? I've been out of the loop for a while

MelissaH: yeah me too!

midori: very good question!

jclark: also I tried b18 today and it has new features that don't show in my usual layout. I was wondering if you could modify my layout so I can test those. It's the don't search obsoletes box and whotnot.

jrichter: The OBO-Edit 1.1 development I've done since the consortium meeting has been tricky, focused bug fixes. I'm still trying to fix an incredibly painful link filter interface bug, and I just tracked down an insidious reasoner problem. So there hasn't been much room for targeted testing.

jclark: they look cool.

5:45 PM

jclark: sorry I didn't mean you testing I meant us

jrichter: Jen - try picking the "Use default layout" option in the Configuration Plugin. The default layout is a lot like yours, and it has the new buttons.

jclark: ah!

jclark: thanks.

jrichter: I don't know what the ole' users have been up to.

jclark: Does someone in the group know?

jclark: I've been travelling a lot and got out of date

jclark: who has been using the betas?

j-lo: i've been using b18 quite a lot

tberardi: I haven't tested since b17.

MelissaH: I've been using b18 a lot the last week

hjd_mgi: I've been using it for browsing during annotation, and the occasional term. I'll be using it today to fix some defs

kchris: I've used b18 a little, I think I did my last set of edits with it.

jrichter: Just to make it clear, beta18 has a horrible reasoner bug. Don't trust the beta18 reasoner.

midori: I've done some editing in beta18 ... term adds, moves, etc. And I did a very quick check on the cross-product tab.

MelissaH: that would explain things!!

hjd_mgi: I'm still not happen with performance during a save, even with the editor checks turned off

MelissaH: yeah, performance has been terrible for us too/

jclark: so should we wait for that fix and then do some concerted testing?

jrichter: Is there anyone who *doesn't* have performance problems while saving?

jrichter: (I'm trying to figure out why I can't reproduce this on any of my machines)

midori: For me saving is back up to essentially the same speed as 16 and previous (but 17 was unusable).

jclark: I haven't tried I don't think.

midori: ... both with checks on and off -- b18 "pauses" to do the checks, but for the same amount of time as b16

j-lo: my save's fine

kchris: I don't think I noticed anything other than the fact that the checker-thing (sorry spacing on what it's really called) is very slow, especially with so many minor errors

MelissaH: my performance isn't so much save as it is opening many paths.

midori: (Yes, I actually timed it. I'm a geek.)

5:50 PM

hjd_mgi: Is there any correlate with mac tiger platform?  I don't remember 16 having any lags

kchris: I did notice that when I did my last edits, which involved adding a lot of paths, that it became VERY VERY SLOW to open paths, but I opened some of the same paths in the official version and it was slow too

MelissaH: it keeps crashing the cell ontology.

MelissaH: because the CL has soooo many paths.

midori: That reminds me ... I've noticed the DAG viewer not updating promptly when I commit a change. (I haven't put in a bug report because I thought John knew about the problem from the Hinxton hands-on session.)

jrichter: So the problem here is the DAG Viewer, yes?

midori: Harold, are you using tiger? Jane and I are.

MelissaH: I think so.

hjd_mgi: I haven't had issues iwth CL; maybe I have an old version (Oct 10 2006)?

hjd_mgi: yes, I'm using tiger

jrichter: And you're actually using the DAG Viewer as you edit, right?

midori: hmm, argues against a big-cat correlation, then ...

midori: John - yes.

MelissaH: We did get a newer version from Minna, not sure if its up on sourceforge yet.

MelissaH: But there aren't that many changes.

jrichter: Here's what I'd like to see...

jrichter: Melissa: Can you send me a copy of the cell ontology that you're using, along with a list of things that I should do to bring about some of the really bad performance you're describing?

MelissaH: happy to.

midori: I just tried a quick test now: I added a term, and when I hit 'create new child', <new term> appeared in the DAG viewer. But when I gave it a name and committed (I've got autocommit off), the DAG viewer continued to show '<new term>'.

kchris: I saw that too, I had to click on some other term to get it to update

5:55 PM

midori: yep

jrichter: The DAG Viewer problem needs to be fixed in OBO-Edit 1.1, it seems. If it's taking so long that it's providing misleading information, we need to do something about it.

midori: Fixing it would be  a Good Thing (tm), I agree.

kchris: I wouldn't say it's taking so long that it's providing misleading info, it just doesn't show anything till it loads, but I agree that fixing this would be great

jrichter: The DAG Viewer tries to calculate the paths in the background, and I'll bet that this is some kind of thread synchronization thing.

midori: That's what you said in hinxton too.

jrichter: Back to Harold's problem...

jrichter: Does anyone else have the problem where there's a long pause before saving, even with all the verification checks disabled?

midori: I don't.

MelissaH: nope

midori: (I also no longer have the beta17 problem, which was that save progress was agonizingly slow.)

hjd_mgi: I will actually time it today when I use it to make some def changes; I'll post it to the group

jrichter: Harold: once the save gets going, the speed is fine, yes? It just takes a long time to start?

jrichter: Also for Harold: You're saving to a local disk right? Not an NFS partition or some kind of virtual network disk?

hjd_mgi: Once the screen actually comes up with where and how to save it, it's fine; and yes, it's a local disk, not virtual

midori: I just tested, and got no detectable pause (ten 10 sec to save).

hjd_mgi: ok, let me try now

6:00 PM

jrichter: Okay. Harold, can you (once again) zip up your config directory and send it to me. Also, please open the verification plugin configuration screen and send me a screen shot.

tberardi has to go to her 10 am meeting, will catch up via transcript

jrichter: Bye Tanya.

midori: bye Tanya

midori: My test did remind me of one other thing:

Alex_MGI: I have only a 10-sec pause myself.

hjd_mgi: ok, 10-12 seconds from uinsg file, save as (all verification off)

midori: beta18 keeps resetting to "write current id rules", even with save profiles that have been set to "don't write id rules".

jrichter: Midori - That's just an interface thing?

midori: Jane has been contemplating what to put in a bug report about the problem (under what circumstances it resets, etc.)

midori: John - not a-tall sure I understand the question.

jrichter: It saves correctly if you remember to set it back to "don't write id rules"?

j-lo: oh yeah - it doesn't reset every time, just sometimes

midori: Oh, yes -- it does respect what the pulldown says. It's just that what the pulldown is set to changes without human intervention.

j-lo: I think it's when you save with a filter, and then then when you turn the filter off, that menu re-sets

j-lo: perhaps

6:05 PM

midori: That can't be it -- I'm having the same problem, and I haven't saved with a filter in ages!

j-lo: not that then

jrichter: This deserves a bug report, in any case. If you can learn more about how to make it happen, we can update the bug report later. I'll see what I can do to track it down on Monday.

midori: I also think I'm not having the problem all the time ... I wonder if it's how I quit OBO-EDit (I often use command-Q, once I've got all the settings the way I want 'em).

hjd_mgi: I had a similar problem a while back with my dbxrefs, and noted that it happend when I would switch back and forth between 1.002 and 1.1betas.'

hjd_mgi: Just timed with verification on: 2.5 minutes + for the warning found screen to appear'

midori: oh wow -- mine's more like 20-30 seconds.

jrichter: Electromagentic signals move a wee bit slower up in Maine.

hjd_mgi: it's the cold

jrichter: Should we move on to Chris's paper responses?

hjd_mgi: yes

midori: OK

6:10 PM

MelissaH: sure

jrichter: I'm not sure what the process is at this point. Would a more experienced publisher talk us through?

MelissaH: What did the editor last tell us, to resubmit with changes, or to submit elsewhere?

MelissaH: Its been so long that it will be a whole new review.

midori: Resubmit with changes within 90 days ... that was on Nov. 14th (who can do the calculation quickly -- are we too late yet?)

kchris: about 3 months, we probably have a few days

Alex_MGI: Just about

jrichter: We have < 1 week, I think.

MelissaH: Then ASAP, we send back with Chris suggested changes and comments. I can help with this.

6:15 PM

Alex_MGI: If you need to add another page, Bioinformatics may allow this but assess a page charge.

MelissaH: His comments were very helpfuland couldn't have come from any of us I don't think.    

midori: I just added up ... if I got it right, we have until Monday.

jrichter: !

jrichter: Great.

midori: from the email: "The system will automatically remove the revision option if a revised paper has not been submitted within 90 days of the original decision. If this happens, a new submission will need to be made."

jrichter: Okay, I've got the latest drafts on my machine, so I'll make the actual changes to the paper and send it around to the working group for comments tonight.

Alex_MGI: A new submission might generate nicer reviews.

Alex_MGI: Or not.

jrichter: Can someone forward Chris's email to me? I don't seem to have it in my inbox.

jrichter: ?

hjd_mgi: If the issues are addressed to the satisfaction of the editor and reviewers, then it would be a definite accept. Otherwise, we start from scratch

midori: on the way ...

MelissaH: I think (hope) the editor will take into account Chris' comments about that (ugly)reviewer.

jrichter: Everybody MUST look at the draft I send around tonight, because we're out of time. I'm resubmitting tomorrow morning no matter what.

jclark: cool app corroborates midori's counting: http://www.jeffpalm.com/dayssince/

jrichter: Midori: Can you be available on Skype tomorrow until around 6pm (your time)? In case I have any questions about the submission process?

6:20 PM

midori: I think so ... I'll keep you informed if I have to go away from skype between, say 3pm and 6pm.

jrichter: You know, now that I look over Chris's email more carefully, I think it needs to be edited before we can submit his comments to the journal (to take out some of his snarkier insider comments, say).

MelissaH: definitely.

jrichter: Would anyone like to sign up for the task of drafting the edited response?

MelissaH: I can help prepare the reply to the editor.

Alex_MGI: But in general, his comments are quite good.

MelissaH: Why don't I take a first stab, and then Midori can edit?

midori: ok

jrichter: Sounds good. Would you be able to send out your draft by tonight, Melissa?

midori: That would let me deal with it tomorrow morning, UK time.

MelissaH: (it just took 65 sec to load 638 paths to 'gamma-delta intraepithelial T cell'

MelissaH: yes

jrichter: A quick style question - do we present our response to the editors as "an edited version of Chris Mungall

jrichter: 's responses" or...

jrichter: do we just present them as "this is what we, the authors, have to say in response"?

MelissaH: You can sign it yourself, but say the authors respond....

kchris: I think it should be from we the authors

hjd_mgi: It should apply to all of  the lised authors

hjd_mgi: llisted

hjd_mgi: listed   #!!#%%

jrichter: Consensus! Sweet.

6:25 PM

MelissaH: You are the corresponding author, but all authors are responsible for all aspects of the paper.

midori: I agree ... the editors will care about (1) what it says and (2) the fact that all authors are behind it.

MelissaH: (held accountable)

Alex_MGI: (Melissa, I just loaded that term and it was almost instantaneous, with the reasoner on)

MelissaH: on b18?

MelissaH: this is happening on two of our windows machines here.

jrichter: Any other issues before we go? I now feel the crushing weight of a billion urgent tasks.

Alex_MGI: on b18, latest publically available Cell Ontology

midori: In that case, our work is done.

MelissaH: hmmm, my reasoner is off, anything else?

MelissaH: one thing is that I have a global renderer on with a bunch of terms marked as a cell slim category.

Alex_MGI: It was the same with the reasoner off.

jrichter: Melissa - It's probably the fact that it's Windows. I think Windows may be having a problem with the way the DAG Viewer does its threaded screen updates.

Alex_MGI: No global render here.

kchris: I had some similar problems with very slow loading of paths, on Mac OS X, and my term only had 214 paths

jrichter: I'll see what I can do about this on Monday. I'm sure it's the threading, and I already have mapped out some strategies to fix it.

midori: I've also had paths load slowly (tho I haven't had anythingake quite as long as that cell term).

jrichter: Now I must go. I've got a ton of stuff to do.

Alex_MGI: Bye.

jrichter: Goodbye, gentle working group. See you in two weeks.

midori: OK, see you all in two weeks!

jclark: good luck

kchris: bye!

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MelissaH: ok, I'll send along the revised reply to Midor,John and Chris ASAP.

jclark: bye

midori: I'll send the transcript as usual.

kchris has quit the server saying: Quit: I'll be back!

6:30 PM

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MelissaH: btw, sorry all that I have been away in CARO land for the last few months....shirking my oboedit duties.

jclark: bye

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MelissaH: see ya.

hjd_mgi:  - happy

hjd_mgi: good bye all

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