OE IRC 23Feb06

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midori: hmm, if no one else turns up, the chat technology could be kinda superfluous ...

jclark: Yup. I'm doing a spot of bug checking while we wait.

jclark: no bugs so far...

jclark: I'mhaving fun here with exciting three-colour renders but repidly discovering that my screen is not large enought to show the whole set of render controls at once. I wonder if John could make the search and render window pop out

midori: I seem to remember all of us using Macs had that problem ... he said something about adjusting the layout xml to deal with it

jclark: I'll have a look at the help guide on xml stuff

midori: I tried playing with the layout a bit, and I could specify a big enough search window height to see all of the controls ... but then the search box took up an awful lot of space, and it was a fixed height, so took up the same huge amt of space with rendering off

midori: maybe a pop-out-able window would be better

midori: oh yes... Hi Petra!

pfey: hello! I'm actually in a different meeting and just tuned in to see what's going on..

jclark: pop-out-able certainly would be good

midori: not much happening yet, and John won't be able to come ... but some of us have decided to chat anyway. We can give John a to-do list afetrwards

jclark: when I click on 'customizing the interface' in the help guide there is no text there.

jclark: sad...

midori: (I'm typing as well as ever :P)

jclark: me too

jclark: do you have any text in that section of the help guide?

midori: um, hang on, lemme look ...

pfey: good - so I just 'listen' in and save it later!

midori: nope, nothing in either of the customization sections

kchris: Between being slightly late and technical difficulties, have I missed it completely?

midori: No, there really hasn't been much yet.

karen: hello sorry to interupt - has anyone else made cross products yet?

jclark: nope

pfey: pascale - did, but she is on the same phone conf as I we don't have the time today

kchris: No, not me. I still need to get input on my SourceForge item to determine if I even need them.

jclark: shall we take notes of pertinent points for john?

karen: oh. They just float as roots. I wondered if this was normal?

midori: No; I tried playing with the cross-product plugin once (a few versions ago) and didn't get very far. I still don't know whether it was because of bugs or just because I didn't have a good idea what I was doing.

karen: I think they are very useful. I can make terms like engineered_gene by combining engineered and gene... I just need to work out where to put them now I have made them.

midori: I'll have to try again now that there's something on cross product in the user guide.

midori: (tho still nothing on the plugin specifically ...)

jclark: is this enough people to start the meeting properly?

karen: Theres a users guide? Where?

midori: In O-E, in the Help menu, click 'user guide'

karen: I have to go to another meeting. Have fun.

midori: OK, it looks like this is all we're gonna get.

midori: Who's worked with beta16?

jclark: me

jclark: are there only two of us actually at our computers?

midori: I can't tell any more ...

kchris: I'm still here. I haven't done anything with beta 16 yet, I'm just downloading it now, and I'm on a new desktop G5 with a new type of mouse that keeps doing things I don't expect, so I feel a little technically challenged today

jclark: Oooooo!

midori: mighty mouse? took me a while to get used to it too.

jclark: I haven't had any problems with b16 yet I don't think.

kchris: I was wondering what the little tiny button on the top did. It does make the dashboard a bit more accessible to have it come down right from the mouse.

midori: I've only done a little bit with it, but that bit has gone fine.

kchris: Maybe we could talk a little about what the criteria are for deciding when a version is enough. Mike seemed a bit concerned at a meeting we had here at SGD last week that we're still using beta versions to commit. When this came up on email, he felt that the consensus by people like himself and Ashburner was that we should not be using betas to commit.

kchris: How far are we from having a release version?

jclark: I think b16 is looking very good

jclark: for me it's much better than the DAG-Edit that is the release version

midori: I agree, beta16 is looking good, and we could probably release it soon. I hope John will be able to finish the User Guide before it's released, though.

kchris: How far is the User Guide from being finished?

jclark: much of it is empty

kchris: Do any of you know enough about how it works to help with writing some of the documentation?

jclark: I suppose so yes

jclark: I think that John ought to do that though while we get on with editing.

midori: As for committing with betas ... there seem to be two schools of thought, and I'm hoping I won't have to take sides. Mike and some others don't want to use betas to commit (understandable, and Mike's explained the position). But some of the working group are chafing at delays in using new versions.

kchris: Personally, my biggest issue is that the format of the file produced by the version being used to commit is not different from the format of the file produced if you used the official version.

midori: I don't think it would be very practical to go back to DAG-Edit for GO; file format is one of the main reasons, as is DAG-Edit performance on our older machines. But once we have a release of OBO-Edit, we should stick to it and not use betas to commit thereafter.

jclark: it seems to me that the advantages of obo-edit far outweigh the disadvantages of not having the help guide completed

kchris: Sometimes there have been big differences, and sometimes there have been "dirty" switches, where some people have switched to the new version, while others have not, with the result being inconsistent file format

jclark: that is a different issue I think

midori: Jen - true for us, but the rest of the world should not be subjected to the horror of incompletely documented software

jclark: We need to figure out what it will take to get obo-edit ready to release

jclark: true

jclark: is john working on the docs?

midori: Karen - I agree, and for that reason I'd like to see a more defined procedure for switching (regardless of whether betas are deemed eligible or not).

kchris: For the rest of the world, having a decent User Guide might be important. Though I'm fine with OBO-Edit now, the first time I opened it, I had no clue how to make it do some things that DAG-Edit had done.

midori: As far as I know, John regards the documentation as a top priority.

jclark: the main problems seem to be obo-edit v. dag-edit

kchris: Midori- I, and I think also Mike, will be happy with your suggestion to not use betas any more after we get a release version out.

jclark: isn't it up to john to get obo-edit ready for release?

kchris: So, we're back to exactly what we need to declare a release version

jclark: yes

kchris: Jen- Yes, but I think it's up to the whole working group to decide what are the criteria for declaring the release version

jclark: cool

jclark: should we reconvene when they are all free then?

kchris: One other thing I wanted to add that we should add to the test suite. Mike uses the software to generate the old format flat files, so we need to make sure that this works. I'll have to check wtih Mike to make sure I understood correctly, but we should include MIke's needs into the test suite.

hjd: I just got here! Iwas trying to use the "Conversations" program that JR orginally used

jclark: hi Harold. We're discussing what we need to do to get obo-edit ready for release

midori: re Karen's comment about betas: I hope the rest of the working group will be as happy -- but just last week Jane mas arguing against even announcing version switches on the mailing list!

jclark: yes. I think we sometimes feel few people use it

midori: Hi, Harold! Welcome to the small group of diehards!

kchris: re version switches: I think we have to announce them, but if we are more careful about our testing, then I think it will be less of an issue

jclark: perhaps john can give us some idea of how many people use obo-edit intensively?

jclark: Yes I sgree we need to handle switches crefully

hjd: Do we have any info on, for example, if people are even still downloading DAG-edit as opposed to OBO-edit?

midori: Might be a thought .. it's dead easy to see how many people have downloaded it, but no telling whether they're doing anything with it once they've got it.

jclark: true

kchris: Jen: You're probabably right, not many others use it. For a while the use version switched so often that SGD curators who used to edit felt they couldn't keep up. Now, none of us edit at all. After the webinar, Rama and I now feel almost up to speed

jclark: that's useful to know

midori: I think one of our aims should be to prevent that sort of situation arising again.

jclark: when we're testing intensively and we find that nobody has even bothered to download the beta it makes us feel a bit as though there's no point fussing over what others want/.That may be wrong.

kchris: Midori: I agree, that's one of the reasons I've been pushing against switching so fast

midori: I really want everyone who's in GO but not in the working group to feel sufficiently informed.

hjd: One of the reasons that I finally got CVS access etc. on my Desktop was that the software people were tired of constantly haveing to install new version fixes whenever a new version was released. Now, it's my problem not theirs

midori: ... and there was much rejoicing.

jclark: I think there's a big difference between leaping at new beta versions and still having DAG-Edit as the release

jclark: it's sensible not to leap into moving from b14 to b16 but still having obo-edit not released after all this time seems a bit daft.

hjd: At one point, however, DAG-edit will need to be retired, as it may not be able to handle everything we are putting into th OBO files

midori: re downloads: I've just discovered that SF will not only tell you how many times something's been downloaded cumulatively, it gives you a history! most cool.

kchris: It does. How much of the OBO betas have had new features, versus just bug fixes?

hjd: Has anyone found any problems with b16 (sorry, I was late); I haven't done anything yet that it has given me a problem with

jclark: at the beginning there were many new features on each new release. No it is mostly bugs

jclark: I've had no problems with b16 though I haven't given it a good thorough testing

midori: it's varied ... and one of the things that Jen (and the rest of us, to be honest) found frustrating was that bug fixes seemed to be waiting while J wrote in new features.

jclark: totally

midori: Harold - those of us who have used beta16 haven't had problems.

jclark: my editing speed has gone way up now I'm on OBO-Edit

jclark: It's great to be able to use it

kchris: Just on a software dev point of view, Bill says that when they're doing stuff, they declare a freeze on new features, then work out all the bugs, then do a release, so if John's been constantly adding new features, that's maybe not the best procedure for getting a release out

jclark: that proceedure sounds a lot better.

midori: We think it's a strong candidate for releas, but I'm holding out for John to finish the user guide (with help form us if he wants it and we can contibute useful stuff)

jclark: could we impose that too?

midori: John seemed receptive to that anyway, so I think we can.

kchris: So for releasing OBO-Edit, we should freeze any new features, b16 seems to have everything the GO office really wants, work out any bugs, and insist on the User Guide

jclark: cool

jclark: yes

midori: yep

hjd: Yes, that sounds sensible

hjd: action item!

jclark: yay!

kchris: cool!

midori: OK, that's one thing we can feed back to John. He'll be thrilled (I mean that seriously, about the release, and facetiously re John gets to write documentation)

midori: Hi Pascale!

hjd: It's currently much better than it was; I had to look something up yesterday and I even found what I was looking for!

jclark: funky

kchris: Yea, he'll love the documentation part

midori: It seems to be somewhere in the vicinity of half done now ...

jclark: now we have an action item can we close the meeting? It's feeding time here.

jclark: yes

midori: Just one more thing: any ideas for the next chat?

kchris: sounds good. I think we accomplished something productive

jclark: I'm eagerly awaiting the xml bit

kchris: Do we want to have a chat about the poster, or just do it on email?

hjd: I think the poster would be good; this seems to work out much faster than email for getting things settled

kchris: There was also a little discussion at the beginning of cross products, and some confusion, so maybe we could get JOhn to teach us how it's supposed to work.

midori: No preference ... I'll bring it up at the next chat if I don't hear anything by email before then.

hjd: Ah, yes, cross-products would be good

jclark: for the poster we shoudl do a graph of how much faster obo-edit runs on our computers than DAG-Edit

jclark: good comedy value

midori: cross prods - Agreed ... I was saying earlier that I'd dabbled once, but didn' t get far cos I didn' t know what I was doing.

kchris: for comedy graphs, we could also graph the speed of discussion by IRC versus by email

jclark: true

hjd: or coming in on some weird discussions in progress....8-)

kchris: I think we're just getting silly now, and the British people have expressed hunger, so I think I'll sign off. I'll save the transcript file

jclark: cool, thanks.

hjd: serious note on poster: something about airtravel, etc. saved??

jclark: good point

jclark: money and time save must be massive

Pascale: hello

kchris: and ease of organization to just do it on a few days notice, instead of weeks of planning

jclark: hi

jclark: yep

Pascale: is the transcript for the first webminar available?

jclark: campaign to move stanford nearer to UK timezone

jclark: what happens when we get a japanses tester?

kchris: I still have files for both days of the original webinar. I think John has posted them, but I can also forward you them directly.

Pascale: yes please, Karen, I would like to have the files

hjd: someone can email me as to how they are saving the log? I can't seem to find how using the IRC applet; maybe I have to use a stand-alone IRC?

midori: Jen - can you collect data for that? DAG-Edit runs too fast on my computer to support the joke

midori: (sorry, got a phone call about the meeting I'm going to this evening)

jclark: sure thing

hjd: ok; same time next week?

jclark: with pleasure!

jclark: yup.

kchris: I am using stand alone IRC. The applet never worked for me. Then it's just the Save as option under the file menu.

kchris: sure

Pascale: oh that's how you do it...

midori: Pascale - yes; Amelia is working on a cleaned-up wersion but I can send you my transcript in the meantime.

hjd: I thought so; I'll have to re-install the other IRC then

Pascale: no I can wait

midori: ok

Pascale: I was wondering if they were posted

midori: poster - yep, I was planning to include a note about these chats

midori: not yet, but I think the plan is to post to the list

midori: OK - are we done? I'll email the list about our action item, and about same time, different week.

jclark: sure

jclark: see you tomorrow

kchris: sounds good

midori: bye all!

jclark: bye

kchris: bye

hjd: e