[DAS2] Notes from the weekly DAS/2 teleconference, 26 Jun 2006

Steve Chervitz Steve_Chervitz at affymetrix.com
Mon Jun 26 17:58:08 UTC 2006

Notes from the weekly DAS/2 teleconference, 26 Jun 2006

$Id: das2-teleconf-2006-06-26.txt,v 1.2 2006/06/26 17:56:11 sac Exp $

Note taker: Steve Chervitz

  Affy: Steve Chervitz, Ed Erwin, Gregg Helt
  Dalke Scientific: Andrew Dalke

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. 

Status reports:

gh: grant update: requested 300k, may get 210-220k. will cover us at
our current burn rate. based on 3mos funding left over from prev
funding, so new request only needs to cover 8mos (through may 2007).
still waiting to hear back. Allocated 30k for andrew's work.
Originally 25k for each of two years.

ad: heard back from suzi from ontology urls. not on das list. will
summarize. spoke to others at NCBO about setting up a service. will
ask Karen Eilbeck (genetics.utah.edu). She only has access to
song.sourceforge.net domain. not good long term because it's dependent
on sf. there is a general domain for the group, but not one she has
access to. what do we want on the pages. xml, html?

gh: meeting suzi this week. can ask more about ontology stuff.

gh: we also discussed moving this das/2 meeting to biweekly.
ad: makes sense. spec vs impl.
sc: should the spec vs impl discussion alternate biweekly?
gh: no, cover everything each meeting.

[A] das/2 meeting will now be biweekly.

[A] next meeting is July 10. No meeting on 3 July (US holiday).

sc: is spec still frozen?
ad: no, just haven't worked on it. if you want to make changes go

[A] steve will fix broken in-page links on the read spec html.

sc: discussed with Gregg last week about migrating affy das/1 server
data to das/2. also experiencing growing pains due to more arrays to
support (the affy das server is in-memory). So we strategized over a
more efficient data model for the exon array data, which eats up a lot
of memory (100-200 MB per array per genome version).

In thinking about it more, seems too ambitious to get the more
efficient data model *and* do the das/2 migration for the July Netaffx
update. Another issue is that we now provide the bgn files as a
separate download from Netaffx, so if we provide bp2 format, users
will have to upgrade their IGB as well (this wouldn't be a concern for
folks launching IGB via java web start, which should be most users).

gh: bp2 format isn't too hard to do. just adds an array id field,
since exon array identifiers are not integers ("1:2345678"). good plan
is to first move to more efficient data model on das/1 to solve memory
issues, then focus on migration to das/2.

Other status  of note:
Allen day has announced the availability of his writeback server:

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