AmiGO-chat-13March07

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gwg: hi Ben, hi Rama

rama: hello

donghui has joined the channel

donghui: morning everyone

eurie: morning

rama: good morning

8:35 AM

rama: we are waiting for jane?

rama: and val?

gwg: and Chris and Seth

eurie: and val

rama: ho yea...

rachaelhuntley: Jane left to work from home 20min ago, she may have forgotten

gwg: does she know the clocks have changed in the US?

rachaelhuntley: i'll send an email to awg

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eurie: I did mention it to her in an email

gwg: she might just be fashionably late in that case

8:40 AM

rama: Seth, no chris?

hitz: we may as well start without him, he has to leave at 9 he said

sjcarbon: it looks chrisless--lemme call...

rama: okay

sjcarbon: has other meeting

eurie: ok let's start then.

eurie: First up: drum roll...

eurie: results of voting on amigo featuures

eurie: Amelia, the envelope?

gwg: I have the results here

gwg: I would do them in reverse order but they're not really all that exciting!

gwg: voila:

gwg: 3) Download option for search results

gwg: ooops,

gwg: those are all the features that got voted on

gwg: I haven't included map2slim, termfinder and IEAs

gwg: the top five were

gwg: Download options

gwg: Search results, sorted

gwg: searching with mis-spelled terms (query suggestion?)

8:45 AM

gwg: Improved gene product search

gwg: and a tie in 5th place between Organize and allow filtering species by kingdom and Advanced Search radio button

rama: I thought we will do the radio button any way

gwg: If all those get done, I will do the other ones that got voted for

gwg: yeah, there are a couple which won't take any time at all

gwg: er, that's ot

gwg: *it

eurie: Cool - any comment about feasibility of implementation of the top 5 for June?

gwg: well, I think Seth and Chris are working on various output format writers, so they should be ok

sjcarbon: working

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gwg: the improved gene product search item is already done in the dev version I'm working on

rama: hi jane

j-lo: sorry - that extra hour fooled me

gwg: lol!

8:50 AM

gwg: the advanced search radio button will be quick

gwg: the filtering species by kingdom one will need extra info put into the database

eurie: Sounds good. cool! we have a plan.

gwg: search results, sorted, will require some searching questions to be asked of working group members

hitz: I can take a look at the species db one once I deal with the IEAs.

gwg: OK, cool

eurie: all right, any other comments on the top five?

eurie: To restate:

gwg: do you have any kind of time frame for the IEAs? Every time it gets mentioned on the mailing list, Mike C. seems to quickly quash any suggestions

rama: query suggestion?

gwg: I will have to ask various questions for that one

rama: i.e suggesting terms when the query is mis-spelled

j-lo: (can someone list the top 5 for the latecomers please?)

gwg: latecomer, you mean?

eurie: Download options, Sorted search results, searching with mis-spelled terms, improved gene product search, a tie in 5th place between Organize and allow filtering species by kingdom and Advanced Search radio button

8:55 AM

j-lo: great. So have we decided to add the enrichment tool and map2slim anyway?

gwg: yep, think so

j-lo: lovely

eurie: ok, if no other comments on the new features to be included in June, we'll move onto the next item?

gwg: go for it

rama: since couple of items from the top five are almost done, do we want to move couple from the bottom five

eurie: I think there's a fair amount of testing and feedback that will likely need to happen for each of these. Especially if map2slim

eurie: and term enrichment are added.

gwg: yeah, I was going to do that Rama.

eurie: we might just want to limit ourselves to these new features to maintain our sanity and testing cycles

j-lo: avoid the usual feature creep

rama: yea, that is lot of testing.

rama: and all these are still going to be AmiGO 1.0?

gwg: we might call some of them AmiGO 1.5

9:00 AM

rama: okay

eurie: So will these features be sent out for testing as they are finished or is there a point when all features will be sent out?

eurie: I mean these 5 we've voted on

gwg: maybe see how it goes

gwg: the little things won't require a whole lot of testing, e.g. the advanced gp search thing

gwg: but things like the misspelling will need to be developed with input from the AWG

hitz: misspelling I think will be quite hard to make effecient

eurie: I think with the current AmiGO, it's difficult to assume that any testing will be "little"

eurie: even "small changes" might have huge unforeseen impact.

sjcarbon: the little things seem to break the most

eurie: joys of amigo 1.0

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9:05 AM

rachaelhuntley: i'd sooner test things as they are finished rather than do a lot of testing all at once

gwg: yes, I think that's probably a better approach

hitz: I think that would work OK as long as we tested on development servers.

hitz: it's a pain (for me, mostly) to do lots of little production releases

gwg: so test on the toy server, do you mean?

hitz: we should probably set up a stanford dev server on the new machines.

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9:10 AM

gwg: I wonder what's happened to Eurie

donghui: are we done with the meeting? there was a long silence.

gwg: we've lost eurie, who was chairing

rama: I have just sent her an email. I will also call her

gwg: thanks rama

eurie has joined the channel

donghui: welcome back

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eurie: oops -

eurie: i had no idea i had been disconnected!

9:15 AM

eurie: i was typing for like 5 minutes

eurie: sniff

eurie: and wondering why no one was saying anything!

eurie: ha

pascale: we're all asleep!

eurie: so did any of the next agenda item make it through?

rama: not yet.

rama: we were talking about testing, setting up dev servers at Stanford

gwg: and then, in a great puff of smoke, you reappeared!

eurie: ok - i just got rama's email catching up on the lost conversation

hitz: we will probably just use the same machine(s), but different url

eurie: so is that the plan for testing?

hitz: the consensus seems to be to test often rather than everything at once. I am not sure that's actually best, though.

hitz: for one, you still have to test EVERYTHING.

hitz: I would think it's easier to test all at once

9:20 AM

pascale: I agree

sjcarbon: but the feedback cycle for the developers is more difficult and shorter if it goes all at once

hitz: of course, it really depends on the individual change.

sjcarbon: for more cosmetic things, the toy servers should be fine anyways

sjcarbon: i would agree that "production" testing should happen all at once

sjcarbon: but that is pretty much a different part of the development cycle anyways

eurie: ok, so it sounds like for some sorts of additions, a smaller testing cycle on toy (berkeley) would be sufficient to give immediate feedback to developers. but "production" testing needs to require testing everything at once.

eurie: so in the last 10 minutes, let's discuss this idea of integrating AmiGO with the rest of the web site better

9:25 AM

eurie: we've made one step of having the base url of amigo and the web pages the same (both geneontology.org instead of one being godatabase.org)

eurie: but do you think we should move further towards integrating the web site and amigo?

eurie: some initial thoughts -

eurie: combining amigo home page with GO home page so that documentation is readily avaialble from AmiGO?

gwg: the GO home page is too messy for that I think

eurie: maybe we need tosimply the GO home page?

gwg: The news items should be cut down to just headlines, I reckon

eurie: Here's another food for thought - does all the documentation need to be front and center for the users?

9:30 AM

eurie: When a user clicks on "Documentation", do they really want to see an "editorial style guide" as one of the first options?

eurie: What sorts of topics and documentation do we want users to have easier and faster and more obvious access to?

gwg: that needs to be moved on to the wiki really, but there's stuff which might be useful for users in it to... it needs sorting out

gwg: it would be useful if for nodes which have documentation, we had a link from the terms in amigo to the docs

gwg: interest groups could possibly be linked up similarly

eurie: yeah, we do link from the evidence codes to the docs.

eurie: maybe we need to link more between amigo and the docs

gwg: but you don't want to take things too far and just make it confusing for the users

eurie: yup, exactly

9:35 AM

eurie: It's not necessarily something we need to decide right here and now. but something to continue to think about - this idea of trying to make navigation among the different web sites of GO more seamless and easy.

rama: yeap, something to think about.

eurie: anyone else want to pipe in on this before we close out the meeting?

rama: any action items?

eurie: I don't think so

eurie: any other items folks want to bring up?

rama: okay, just making sure

eurie: rama, can you email the transcript?

rama: i will

eurie: my window closed out when I got booted

eurie: thanks

rama: bye

pascale: bye

eurie: ok - next meeting March 27th?

sjcarbon: bye

gwg: cyas

pascale: ok

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