[DAS2] Notes from the weekly DAS/2 teleconference, 22 May 2006

[Steve Chervitz]

Notes from the weekly DAS/2 teleconference, 22 May 2006

$Id: das2-teleconf-2006-05-22.txt,v 1.1 2006/05/22 18:07:09 sac Exp $

Note taker: Steve Chervitz

Attendees: 
  Affy: Steve Chervitz, Ed Erwin, Gregg Helt
  CSHL: Lincoln Stein
  U Alabama: Ann Loraine
  UCLA: Allen Day

Action items are flagged with '[A]'.

These notes are checked into the biodas.org CVS repository at
das/das2/notes/2006. Instructions on how to access this
repository are at http://biodas.org

DISCLAIMER: 
The note taker aims for completeness and accuracy, but these goals are
not always achievable, given the desire to get the notes out with a
rapid turnaround. So don't consider these notes as complete minutes
from the meeting, but rather abbreviated, summarized versions of what
was discussed. There may be errors of commission and omission.
Participants are welcome to post comments and/or corrections to these
as they see fit. 


Topic: status reports
---------------------

aday: working on converting xml to sql for the writeback
functionality. Need to bind to apache. should be done today.

gh: would like to test writeback into IGB.

aday: will give url to gregg. if you post an xml doc to that url. will
get back a response mapping provisional names to persisted names in
the db. 

gh: editing too?
aday: no, creation only, at least today. maybe editing later this week.
gh: I could get some writeback for creation in igb this week. with
effort. 

aday: currently writes yeast and human features to the same data
source.   
gh: fine for testing. will focus on human.

sc: probably should just send to url to gregg then to send to list
once we test it a bit.

[A] allen will send info to gregg re: accessing his writeback server

gh: turning on curation in igb. need to connect to das
writeback. previously wasn't connected. given I have a das writer it
should go smoothly. aiming to get something going this week.
Not checked in. Still struggling with sf cvs change.

other news: applying for no cost extension to current grant. have
100-200k left. still determining. need to get app for extension in
today. this is more than we though. should last at least another
couple of month. will let folks know when we know.

ls: pretty good.

gh: will contact p. good about bridge funding until new grant is
funded. working with suzi to re-submit in October with her as PI.

sc: sf cvs trouble?

gh: hangs my jbuilder ide now. I updated repository information in CVS
Root files using perl. JBuilder doesn't like it.

sc: I did the same sort of perl-based editing of CVS Root files and it
worked for me.

al: Doing overrepresentation analysis for QTL studies.
Usually this is for microarray analysis, where you want to see what
things the expressed genes they have in common. you collect GO
annotations, if you see some recurring in the list, you infer that that is
important/involved in the process.
We want to do overrepresentation alaysis for gene assoc studies.
look for go terms/ pathways represented in the list of gene
associations. having trouble getting a null model. plan to hammer on a
das server to get a null distribution. would that be ok? thinking
about using the UCSC das server.

gh: would be a great test to see how they handle lots of
queries. 

ls: also try the biomart interface at ensembl. das feeds into it
internally. there are api's for variety of languages, or can send sql
to it. try the ucsc das server first.

al: is there a contact person for ucsc das server?

ls: jim kent.

aday: write to genome mailing list. they're responsive.

al: top page of das server has message that implies it's not
well-supported. 

gh: the things you're interested in will do fine (txts, rna, gene
predictions). doesn't do well on extra stuff in their db (fastcons
conservation scores across regions of conservation, expression score,
etc). For basic annotations it works fine.

al: most interested in the "knownGene" data type. das server gives
back accessions. annotations are encoded. need to look up entrez gene id
from accession. using NCBI mapping files to get mRNA accessions.
then get ontology annotations, also distributed via NCBI.

gh: in das/2 this is handled better with xids (this das id = that
entrez id).  
al: will ucsc update their server to das/2?
gh: more likely after grant renewal.

al: affy server?
sc: we have knownGene annotations.

al: doing this for a statistical genetics class this fall. expect lots
of hits on the server then.

[A] Ann will test hammering on the affy das/2 server before turning her
students loose on it this Fall.

sc: no writeback related work, but attended the JavaOne meeting last
week. Some things of interest to our work:
1) Presentation on the ATOM protocol and REST in general. Mentioned
   something called WADL that is a REST-based web service to automate
   client-side interactions. Seemed more general that ATOM since one
   can use it to implement ATOM.
2) Eclipse RCP (rich client platform). Is a gutted version of the
   Eclipse Java IDE with all the java tools removed. You're left with
   lots of core functionality that can be of use for any java app. Was
   used by NASA when they needed to integrate lots of heterogeneous
   apps related to the Mars space mission. Seemed like we have a
   similar situation with IGB + Apollo integration. The Eclipse RCP
   gives you a framework for assembling tightly integrated components
   that are loosely coupled.

gh: do all the components need to be eclipse plugins?
sc: yes (believe so). not sure how much work that entails.

gh: I looked at using eclipse and netbeans back when starting to
develop IGB, but that was a long time ago. might be worth looking
again. 

sc: there's a new book on building Eclipse RCP apps. On my desk.

[A] gregg will look into the eclipse RCP as a possible app framework.

3) Extreme GUI makeover talk was interesting to see what you can do
   with Java 2D to dress up a "plain-jane" application. This year,
   they created a suped-up version of the Thunderbird email app. There
   are other enhancements coming with the next java release that
   improve java on the desktop (version 6 called  Mustang, due in
   October). 

4) java.util.concurrent package in java 5.0 has quite a lot of
   functionality for implementing things in your app that require
   multithreading support. There is a back port to JDK 1.4.

5) Scripting in java was very big. Using the groovy scripting
   language, with simplified syntax but access to all of java.
   AJAX was also very hot.

gh: I saw something using gbrowse and AJAX.
ls: this is an ian holmes project. It has google maps like
interface. change track order by tracking, smooth scroll and and
zooming. the idea is to supercede igb so people can do it on the web.

al: you need to do 1d not 2d zooming.
ls: it does that.
gh: the hard part is dealing with lots of data.

al: I always get questions from people who look at google maps and
say, "how come you genome people can't do something like this?"

ls: it's running now. go to http://genome.biowiki.org/ or look for
"gbowse ajax client" on biowiki.org.


Topic: Next meeting
--------------------
gh: next monday is US holiday (memorial day, 5/29). next meeting will
therefore be in two weeks.