From GO Public
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jrichter: Hi, everybody.
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.
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jrichter: Hi, Karen & Jane.
kchris: Hi John and Jane
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jrichter: David Sutherland said he'd try to show up... lemme quickly email him before we start.
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
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
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?
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
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.
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.
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:
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.
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.
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!)
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."
midori: Looking forward to the "getting started" doc -- I've definitely been feeling clueless in the face of change.
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?
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)
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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.
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: 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.
jrichter: bye all
j-lo: see ya