[DAS2] Notes from the weekly DAS/2 teleconference, 18 Dec 2006

Steve Chervitz Steve_Chervitz at affymetrix.com
Mon Dec 18 18:33:56 UTC 2006

Notes from the weekly DAS/2 teleconference, 18 Dec 2006

$Id: das2-teleconf-2006-12-18.txt,v 1.3 2006/12/18 18:30:56 sac Exp $

Teleconference Info:
   * Schedule:         Biweekly on Monday
   * Time of Day:      9:30 AM PST, 17:30 GMT
   * Dialin (US):      800-531-3250
   * Dialin (Intl):    303-928-2693
   * Toll-free UK:     08 00 40 49 467
   * Toll-free France: 08 00 907 839
   * Conference ID:    2879055
   * Passcode:         1365

  Affy: Steve Chervitz, Gregg Helt
  UCLA: Allen Day, Brian O'connor

Note taker: Steve Chervitz

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

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. 

 * Global Seq IDs
 * Status reports

Topic: Global Seq IDs:
gh: re: global seq ids. would like a page in das2 sources as an xml
format. then we could have this list in the das2 registry so you could
go and look things up rather than just an HTML format.

ee: good. them html could maybe be generated out of html
gh: yes. now it's a wiki page, makes it complicated.

aday: wanted to do a similar thing, automatically process the data. I
have a wiki text parser, partially implemented.
gh: autogenerates from a template somewhere?
aday: a wikitext parser, given a wikitext DOM, you can do what you
need to. can generate something from wikitext rather than put xml into
the wiki.

[A] Allen will help XMLify the das2 global seq IDs wiki page

Topic: Status reports

gh: new hardware for affy das2 server, formal paperwork done, should
get it by end of this week. new year, we'll begin working on setting
it up. will allow us to support more organisms, arrays, and genome
versions. 32g memory.

Other work: last teleconf we talked about serving up affy
transcriptome data via das/2. Have talked to Tom Gingeras about
getting their data as plots on a das/2 server. still need to consider
what formats to support. netCDF?

aday: not using now but know how.

gh: currently in bar format, but would like to consider moving to
another efficient format.
a plugin to the das2 server that doesn't hold stuff into memory. too
much data. phase 3 whole genome in 5bp resolution, 8 cell lines, 3
replicates. lots of data. indexing scheme to the bar format used
internally in transcriptome group. can grab slices of the data

aday: lots of programming overhead to creating a netCDF file. lots of
initialization of the matrix you have to do. loading data in, have to
be aware of how you created the matrix. can only grow along one
dimension. loading needs to be aware of expected growth plan.

gh: splicing returns a self-contained bar file for each slice. could
be a self-contained netCDF file for each slice.
aday: ok. in the order that makes sense for each display. a few dozen
lines to get the thing set up. also, must write file to disk, can't
deal with it in memory only. didn't like. especially when
reading. have to grab it, download to disk, then open it. brian o'connor can
elaborate re: client side. I ran into it on server side as well.

bo: look in assay package for igb codebase or the hyrax client
codebase. haven't been using it for a while. biggest pain is where to
write a temp file given the OS/platform.

gh: continuing my status: IGB release 3 weeks ago, a few problems with
enhancements to read CHP files (affy std for programs that generate
expression data files). need to do another release to address these
problems (tomorrow expected). Also, caching problems with igb given
full URIs for segments, types in das/2 feat queries, file names are
now too long for some OSs. used steve's suggestion of md5 digest on
it. reverse lookup won't work, but not an issue now.
Can now turn back on full uri for types and segments in feat queries,
so it should be able to work with biopackages server.

gh: will be a different genome per server. need to resolve this
(resolution of each genome). Need to move to the proper das/2 approved
way.   working with affy server to loosen restriction on allowed
queries. also some work on editing html docs.

ee: igb release. working on igb manual. now several versions out of
data. First part: going thru existing manual, fixing things not currently
correct. Second part: going thru release notes and incorporating new
things. Working on first part now. Second part by later this week.

aday: nothing to report. funding did come through to CSHL this
week. fine now.
gh: sorry for the lapse.

sc: fixed 502 gateway error (mod_proxy tweak). HTML retrieval spec
docs fixups. wikification of biodas.org with Andreas Prlic.

[A] gregg will do his html das/2 retrieval spec fixes by end of week.

gh: (regarding the apache complaint about a bad header from the das/2
server). Looking at the http specs, header has: http version, status
code, optionally text. that's the only line that doesn't need a
colon. maybe i'm not putting http version at the start of the lines.

gh: on track for devoting most of Jan to das work?
sc: at least half. will know more this week.

bo: not much das/2 work, focussing on graduating! worked on
biopackages build process. automated build process for building
rpms. that has been completed. build farm fc2, fc5, sunos,
i386/686. allows us to build binaries for the das server for different
target platforms and managing dependencies. can do this for the das/2
server.  One server, uses VMware to run various distributions as
virtual hosts to do the builds.

Other topics:

bo: how as response been to frozen spec?
gh: brian G and lincoln are happier. haven't heard from anyone
else. would like to hear from folks in England. we haven't advertised
it except on the list. top priority was helping brian and lincoln
(NCI) statisfied that they can use it. that has gone well. lincoln was
reporting 2 weeks ago that things were going well with brian's
work. looking for server to serve up hapmap data. has client library
in place. was having problems with feat requests, we responded,
haven't heard back. Hopefully we'll hear from them next year.

[A] Next das2 teleconf: 8 Jan 2007

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