OE IRC 31May07

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5:20 PM

hjd_mgi has joined the channel

hjd_mgi: Hello

5:25 PM

Alex_MGI has joined the channel

jrichter has joined the channel

erika has granted operator privileges to jrichter

erika has removed operator privileges to erika

jrichter: Hi, everybody.

Alex_MGI: HI

midori: hi

jrichter: I guess we have 5 minutes until we start. Erika isn't really here. That's a proxy account I set up for her to use.

5:30 PM

kchris has joined the channel

j-lo has joined the channel

jrichter: Hi, Karen & Jane.

j-lo: hello

kchris: Hi John and Jane 

tberardi has joined the channel

pfey has joined the channel

jrichter: David Sutherland said he'd try to show up... lemme quickly email him before we start.

5:35 PM

jrichter: Oh, never mind. He can't make it. We can start if folks are ready.

midori: OK; I'm thinking of this as basically your show.

jrichter: Cool. Here's what's to report:

jrichter: The latest paper is just about out the door. Oddly, the Bio-Ontologies SIG keeps insisting that I'm submitting a poster, no matter how much I insist to the contrary. I'll fill everyone in when I know more.

jrichter: The first paper seems to be stalled, yet again. A few days ago I received an urgent request to fax a permission to publish letter to the journal, but the fax number they sent me is not in service. I emailed them scans of the signed documents, and I haven't heard a word out of them since, despite repeated followup emails.

midori: oh dear

jrichter: Yeah.

j-lo: It always takes longer for these things to get to print that you expect

jrichter: It may be nearly a year from start to finish on this one. Not bad for 2 pages.

tberardi: Tell me about it, Emily, Ev and I (well, mostly Emily) wrote a book chapter a year and a half ago

5:40 PM

tberardi: and it's just going to be published in a couple months.

Alex_MGI: This is the number Bioinformatics sent me for the Licence to Publish form

Alex_MGI: Oxford Journals requires your agreement before publishing your article. Please download our Licence to Publish form, complete and return the form by fax (+44 1865 355741)

midori: Book chapters are the worst ...

Alex_MGI: It worked in February.

jrichter: That's exactly the number I faxed to. I use an online fax service, and their diagnostic team told me that the fax machine at that number was not responding normally.

midori: Yep, that's the same fax number they put in the emails about the O-E paper.

Alex_MGI: Maybe it only likes old-style fax machines.

midori: Do you want me to try faxing them? It wouldn't be international from here; if you send me the scans I can print 'em and shove 'em through the fax machine.

jrichter: I was just typing the following: Midori, if I sent you scans of the paperwork, would you be able to print out and refax the pages?

midori: snap!

jrichter: I'll email those to you as soon as we're done.

midori: I'll fax them as soon as I get in tomorrow.

midori: (chatting from home today)

jrichter: I only have one other thing on my agenda...

jrichter: (wait, two things. anyway...)

jrichter: Finally, I released a crippled OBO-Edit 2.0 demo, but it seems like lots of people are having trouble with the installer. Has anyone been able to get it working?

midori: not I 

tberardi: Sort of

jrichter: ?

tberardi: I can load GO and double click on terms to select them

tberardi: but when I go to the graph editor

midori: ... though I did get the platform-independent version up, running, and annoying me with regard to layouts.

tberardi: I just see the three root terms

tberardi: and not the parentage of the term I selected.

hjd_mgi: The PFI version failed to return anything for a regular search.

tberardi: (which is what I'd expect)

midori: I got a teensy bit further than Tanya, but it's clear I"m going to have to practice a LOT more before I have a clue what I'm doing.

tberardi: I downloaded the Windows version and the installer hung

tberardi: but appeared to install anyway

jrichter: Tanya - the graph editor is doing what it's supposed to. You're describing the behavior of the Graphical DAG Viewer.

5:45 PM

tberardi: When I click on that tab I see the words:

tberardi: "ancestor views of termxxxx" but no graphic

jrichter: Huh. What term is selected?

tberardi: I tried 'structural constituent of nuclear pore'

tberardi: so the text says

tberardi: "ancestor views of structural constituent of nuclear pore'

tberardi: and that's all I see

jrichter: Is the reasoner on? If it isn't, try turning it on.

tberardi: reasoner is not on

tberardi: clicking the checkbox has caused the whole reasoner window to go blank

midori: (drat, I don't have the 2.000 layout here yet ... hang on ...)

jrichter: that's okay. It'll come back up when it's done running the reasoner.

tberardi: (I think it's thinking.)

jrichter: While Tanya and Midori attempt to navigate that bug nest, lemme bring up something else...

jrichter: Seth from BBOP has just finished creating a web service that can be used to easily submit new term requests to sourceforge. I could use this service to easily create a plugin to allow new term requests to be submitted directly from OBO-Edit. Would you guys like something like that?

kchris: Personally, that wouldn't be one of my priority plugins.

5:50 PM

jrichter: I guess this is the wrong crowd for that plugin. If anyone here wants a new term, they just create it.

kchris: Well no, we all have to submit the SF item too, but that just isn't hard to do.

j-lo: I think that plugin is more useful for novice users

j-lo: and I'm not sure they'd be using O-E

kchris: I was just going to say, using SF is MUCH easier that using OE.

midori: I can foresee a use for it when cross-products are more widely deployed -- someone could generate a request for a term in a different ontology from the one they're editing (e.g. I decide there should be a new Cell Ontology or ChEBI term). I'm perfectly comfortable creating items right in SF, but I'm not sure I know where all of the different trackers are.

midori: ... But I agree that it's not a sky-high priority.\

jrichter: And, of course, the task of matching an ontology with the appropriate tracker is out of the scope of Seth's code, so we'd have to write that part ourselves.

jrichter: Anyway, I won't waste my time with that!

jrichter: To Karen's comment about OE's ease-of-use:

5:55 PM

tberardi: (update: nothing has changed, am emailing John a screenshot of my view)

midori: Got my 2.000 chugging ...

jrichter: The new graph editor *should* make OBO-Edit a lot easier to use, but I'm really interested in getting feedback on how to make the controls as intuitive and easy-to-use as possible. To that end, I'm going to spend the next week building an OBO 2.0 beta that works on machines besides my own...

midori: I'm still having to restart OBO-Edit to change layouts (the bug report is in).

tberardi: sounds good to me

jrichter: From now on, the OBO-Edit command-line launcher will have a new parameter: -conf

midori: Right now, I'm still new at this. Translation: I have no idea WTF is going on!!

jrichter: You can use that parameter to point to any configuration directory you want.

Alex_MGI: Having it have separate preferences from 1.101 would be helpful.

jrichter: This should stop beta settings from polluting your real settings, and it should make it easier to run multiple versions of OBO-Edit on the same machine.

midori: excellent

Alex_MGI: Please provide a brief description of how to switch between preferences when you send out the next version of the beta.

hjd_mgi: Great, 'cause I'd like to play with it more, but it's a pain to switch back

jrichter: I will. I'll also send out a little "Getting started with the graph editor" memo.

tberardi: somehow I managed to crash it yesterday while playing with the zoom in/zoom out feature

Alex_MGI: (Since I like to launch from the Finder or Dock on the Mac)

midori: ANyway, in 2.000, how can I get a selection or some search results to be the focus of attention in the graph editor?

tberardi: I think I got carried away

jrichter: If you select something in the main view, it should appear and be selected in the graph editor window.

jrichter: Or you can double-click to select something.

6:00 PM

jrichter: You can expand child/parent nodes by hovering over the expand control bar at the bottom of a node.

jrichter: You'll see "expand all/collapse all" controls fade in.

tberardi: maybe we can have a webex demo again??

jrichter: Good idea. The next meeting will be a webex meeting, and we'll do a follow-along-at-home demo.

tberardi: (Sounds good. Sorry, need to run to my 10 am meeting now.  Will catch up via transcript.)

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midori: Um, I'm afraid the selection isn't getting through to the graph editor. I change selections (oh, and I *hate* having to double-click, but that's beside the point) in the ontology editor panel, but nothing changes in the graph editor. 

jrichter: Midori - You're using the layout I mailed around?

midori: And what's supposed to appear in the graph DAG view window? I just get words, like Tanya described, with the reasoner on or off.

midori: That window does update when I change selections, though.

midori: Yes, using your layout.

jrichter: The graph dag view window ought to be showing you a graph of all the parent terms of the selection for each relationship type in the ontology.

jrichter: Anyway, obviously Mac OS is having major issues with this thing. I need to release a new version or two.

midori: Sadly, it's not.

midori: (not showing what it's supposed to, that is ... apparently it *is* having issues!)

6:05 PM

jrichter: IMPORTANT THING: As you test OBO-Edit 2.0, please keep a little notepad with you. Whenever you try something and it doesn't do what you expected, please write down what you thought should happen, and what OBO-Edit 2.0 did instead. It's important you note this right away, so we can make the interface intuitive to novice users.

jrichter: We've covered everything I wanted to talk about... does anybody else have anything?

midori: the cat says: dibxxxxxxxxxxxx

kchris: Yesterday Fiona said "Mommy, that's the cake song. It's not Depeche Mode."

jrichter: Ha!

midori: Looking forward to the "getting started" doc -- I've definitely been feeling clueless in the face of change.

6:10 PM

jrichter: What do people think about adding a "tip of the day" thing to OBO-Edit? It would be easy to add the popup, but we'd have to write the tips...

Alex_MGI: As long as it can be suppressed at will.

hjd_mgi: I hate "pop up" tips of the day!

jrichter: (Maybe it would be better if I sent out tip of the day emails at first or something, and then used them as a database later)

kchris: Those things always just annoyed me in Word..., though not as much as that %$^&$# paperclip.

midori: I just reflexively dismiss those from OpenOffice  and suchlike ... but yeah, as long as they can be turned off ...

jrichter: Sounds like no one wants that. But what about tip emails?

hjd_mgi: better

kchris: but to be able to use them, I'd still have to file them somewhere, better to have them in the Help doc somewhere that's easy to search

jrichter: The help doc only gets updated when OBO-Edit is released, though... How bout on the Wiki page?

midori: I like the idea of accumulating them for a database -- FAQ fodder, perhaps. (No objection to receiving them as email, tho.) Wiki's a good idea too.

jrichter: (And then the Wiki tips can get dumped into the help docs when we do a major release)

MelissaH has joined the channel

MelissaH: Hiya,

jrichter: Holy crap! Someone just added a tips section to the Wiki! You guys are fast

Alex_MGI: Sounds good to me.

MelissaH: sorry so late.

6:15 PM

jrichter: I think we were just winding down.

MelissaH: I'll catch up on the chat history.

jrichter: Anyway, go to http://wiki.geneontology.org/index.php/OBO-Edit:_Tips for your tip of the day.

jrichter: If you notice me skipping a day, please hassle me.

hjd_mgi: Tipse

hjd_mgi: fire alarm! bye

Alex_MGI: Fire alarm here.

jrichter: Run for your lives!

jrichter: In an orderly fashion.

midori: do you think it'll spread to my house?

jrichter: I think we're ready to wrap up. If there's no other business, I'll see you guys in 2 weeks when we do the play-along graph editor demo.

midori: OK; I'll send the transcript.

6:20 PM

jrichter: bye all

kchris: bye

j-lo: see ya