AmiGO-chat-10April07

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>So the IEA instance of AmiGO - what did we think?

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>it's pretty sluggish and overwhelming as is.

<a href="irc://irc.macnn.com/donghui,isuser">donghui: </a>i tried the servers, depending on the term, the search time varies from several seconds to over 30 sec, knid of slow

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>I tested it briefly and nothing is broken as far as I can tell

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>the counts on browse page are off which makes it hard to test terms with ridiculous <a href="irc://irc.macnn.com/#%23">##</a> of GAs

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>It wasn't that much slower than normal AmiGO for me

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i didn't notice a lot of use, so maybe 'slow' people were over lapping

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>we could schedule a time for everyine to hit it at the same time

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>just for fun

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>how about now?

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>right now? =)

<a href="irc://irc.macnn.com/donghui,isuser">donghui: </a>could be, I tested right after the email was sent

<a href="irc://irc.macnn.com/donghui,isuser">donghui: </a>sure

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>go!

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>could you send the url again? save me searching my inbox

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>(sorry!)

<a href="irc://irc.macnn.com/donghui,isuser">donghui: </a>that would be great!

<a href="irc://irc.macnn.com/rama,isuser">rama: </a><a href="http://toy.lbl.gov:9002/cgi-bin/amigo/go.cgi">http://toy.lbl.gov:9002/cgi-bin/amigo/go.cgi</a>

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>cheers!

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>right now 6 processes

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>okay, everyone test

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>12 processes

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>9 and holding

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>pretty painful

8:45 AM

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>I think the association details pages need to be organized

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>especially the gene product searches

<a href="irc://irc.macnn.com/donghui,isuser">donghui: </a>I tested the term kinase, there was a noticeable delay in getting result

<a href="irc://irc.macnn.com/cjm,isuser">cjm: </a>Seth - I haven'tperformance should be easy to benchmark with and without IEAs in an objective way. do we not have some scripts for this....?

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>searchs are slow in all versions though.

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>we have a timing branch, no?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i could get some performance scripts ready

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>also, our new amigo-dev machine arrived yesterday

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>the timing branch was just for individual use

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>they would be great to test new loading/old loading

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>you wouldn't want to be in a situation where your life depended on getting the results from an AmiGO gp search... (something that happens to me all the time, obviously)

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>so it sounds like this is currently too slow for our needs

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>if everybody went and hammered on amigo right now, would it also slow down?

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>let's give it a go!

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>I just checked gowebs loads are <1

8:50 AM

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>i think like Chris says, it would be good to get an objective view of how much slower the full load would be

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>there are so many variables here that I don't think it's really all that informative to be testing like this

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>I agree with amelia and chris

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>it does seem subjectively slower

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>okay - so do we have a way to do this?

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>measure speed i mean

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i can write that

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>Okay, great. Action item for Seth

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>the associations page has to be organized. We should have a summary table of associations like the annotations table on the GOC site and let user decide which ones they want to view further

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>which do you call the associations page?

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>yes, I agree - there are too many results with IEAs

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i think the issue is getting the summary table without doing as many joins

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>yes 184 pages of associations = useless. We have filters, but if they are "mandatory" it should be more explicit

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>the results page

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>the page you get when you click on the View associations

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>term associations? gp associations?

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>term associations

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>term details page

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>yeah, i think in terms of user experience, the current results page when you search on gp or view associated annotations is too overwhelming

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>seth, we probably need to put this in a view

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>that would be great

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>unless there are some clever indexes (indices?) we can add

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>make the API easier too

8:55 AM

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>The 'view all results' doesn't retrieve 45 pages of results by the way

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>I don't know what you guys are talking about (Ben and Seth)

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>in sql you do joins across multiple tables. We need to do this for the summary table (results) in current schema.

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>ways of making the searches return faster

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>a "view" (and please correct!) is just a fake table in the database which is the result of a select statement - in our case joining across tables.

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>I see

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>You are basically trading memory/disk for CPU time

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>chris and I have already talked about this

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>I have to confess, I have never actualy MADE a view.

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>so this is changes to the actual database itself?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>no

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>it adds a 'fake' table

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>this table is created on the fly i think

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>no it is not

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>so this would be for AmiGO 2.0 really?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>not in mysql anyways

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i think it could be used for both

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i'll try making views this week

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>why don't we just create views for the various go db objects now? I think it would make life much easier

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>it's not really a schema change, but they do have to be created in the database; presumably at loading

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>I think this should be an action item for SW group to figure out who and when

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>sounds good

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>ok

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>chris? comments?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i think he's mulitasking with a phone call right now too

9:00 AM

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>so the action item is for the SW group to look into creating views for the database?

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>and report back

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>?

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>Is it the plan to worry about the format/details of a table on the webpage later?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i'll email the list and see if i can get it added to the agenda

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>Rama, yes I think so

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>Seth - great

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>Okay, anything further on IEAs, or shall we move on?

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>okay

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>Download option?

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>Will that also be solved with the DB 'views'?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>no, but it may be speeded up

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>which download option Rama?

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>Having a button to download 45 pages of annotations to your desktop as a excel file (maybe)

9:05 AM

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>I don't think Excel is on the list, but I'm working on adding new filters and fixing some of the older ones

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>right now I'm adding GO association

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>i gave excel as an example. tab delimited will work too

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>we already have this in both the AmiGO 1.0 and 2.0 plans I think

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>shall we move on to the boolean searching?

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>excel is just comma-delimited (.csv)

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>and of course, excel can read tab-delim if user has 1/2 a clue

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>I agree Ben

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>GO assoc is tab-delimited

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>I don't think Go assoc is a useful format for anything other than GOA.

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>BUT maybe it's the easiest way to handle NOTs/etc.

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>But we've already defined the GO assoc file so why not use it instead of generating a new file format

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>there are extra columns which will make little sense to naive juser

9:10 AM

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>I agree with eurie. It is easy to dela with the GO-associations file.

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<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>good points. question is: is loading a GOA file into excel useful?

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>and basicaly we are using amigo as a very overwritten "grep"

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>sure someone might download the whole GOA file but a download option allows someone to only download aspergillus annotations without having to download all of GOA.

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>espeically those users who don't know how to grep

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>this is the audience we need to be meeting

cjm has joined the channel

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>this is the audience folks in the outreach group have been trying to get involved in submitting annotations

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>yes, thanks eurie

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>ok I'm convinced. and I am resisting comenting on the download thing

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>why go through the effort of getting groups to submit annotations if they have to know "grep" to see them?

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>absolutely - we need this feature

9:15 AM

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>Right, lets stay on target people - we have 15 minutes to discuss boolean searchinh

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>g

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>so, how have people found the boolean searching

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>?

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>I am assuming download option is going to be looked into?

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>@rama: yup

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>(rama - downloading is a big feature - we will definitely do it)

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>okay. thanks

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>Seth - does the boolean search allow wildcards?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>not in the middle of words

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>that wouldn't be hard to add though

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>cool

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>that was the only thing i found lacking

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i was mostly concerned with the grammar,

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>but I'll add that and repost it

9:20 AM

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>I found the grammar pretty intuitive

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>great!

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>any other comments on that?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>i assume '*' is an unused character and therefore safe for me to use as a wild card?

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>% is also used

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>presumably you wrote the parser from scratch for the boolean search?

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>yes

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>simple and reusable--already in a module

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>cool

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>so Seth, you're going to send round another email about the boolean grammar did you say?

9:25 AM

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>after i add the wildcard

<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>sounds good. i haven't had a chance to test it

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>no problem--be aware that it is slow for testing purposes though

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>great, we can discuss next time then

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>anything else anyone wants to bring up?

<a href="irc://irc.macnn.com/hitz,isuser">hitz: </a>not it

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>okay, I'll post some notes about this meeting on the wiki

<a href="irc://irc.macnn.com/j-lo,isuser">j-lo: </a>and see you all next time

<a href="irc://irc.macnn.com/sjcarbon,isuser">sjcarbon: </a>see ya!

<a href="irc://irc.macnn.com/cjm,isuser">cjm: </a>bye!

<a href="irc://irc.macnn.com/rama,isuser">rama: </a>thanks. bye

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<a href="irc://irc.macnn.com/eurie,isuser">eurie: </a>bye!

<a href="irc://irc.macnn.com/gwg,isuser">gwg: </a>cyas

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