[DAS] Minutes from 30 Oct 2008 DAS teleconference

Thu Oct 30 18:56:43 UTC 2008

Action items are now summarized at the end of the minutes.

Steve

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Minutes from 30 Oct 2008 DAS teleconference

Teleconference Info:
   * Schedule:         Biweekly on Thursday
   * Time of Day:      9:00 AM PDT, 12:00 PM EST, 16:00 GMT
   * Dialin:           See biodas.org community portal page for details

Attendees: 
    Free agent: Gregg Helt
    Affymetrix: Steve Chervitz
    EBI: Andy Jenkinson
    Sanger: Jonathan Warren, Felix Kokocinski
    U North Carolina: Ann Loraine, Steven Blanchard, John Nicol

Note taker: Steve Chervitz

Action items are flagged with '[A]' and are summarized at the bottom of the
minutes.

The teleconference schedule and links to past minutes are
available from the Community Portal section of the biodas.org site:
http://www.biodas.org/wiki/BioDAS:Community_Portal#Teleconference

DISCLAIMER: 
The note taker aims for completeness and accuracy, but these goals are
not always achievable. 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 on the the discussion list.

========================================================

Agenda:
========

* Review progress on action items from last week (based on minutes)
* Gregg give overview of the Trellis/Ivy DAS1-->DAS2 proxy, and future plans

Discussion of action items from 16 oct 2008 teleconf:
=====================================================

Previous action items are underlined, with relevant discussion below.

Suzi: Decide Ian or Suzi is PI on grant. Issue reciprocal letters of collab.
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(Pending)  - Suzi is not on this call.

Steve: Combine das and das2 lists. Can they be merged.
--------------------------------------------------------------

SC: Plan is to ultimately have a single das discussion list. Everyone
on das2 list that is not on the das list will be added. Then we can
redirect any posts to the das2 list to go to the das list. Das2 list
will be retained as an archive.

I have been added as an admin on the das list, so now I can work on
migrating users. Also need to update the list description per the new
arrangement.  Haven't had a chance to do this, but will get on it by
mid-next week.

Noticed a fair amount of spam sent to the list that needs
moderation. Original moderators are no longer active.

AJ: We can have the list auto reject messages from non-subscribers.

SC: Good idea. Will reduce moderation burdon.

AJ/JW: Willing to be added as moderators.

Suzi: Summation of authentication pros and cons. Review descriptions, make a
decision.
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(Pending)

Gregg will forward our off-list discussions to the list to get input from
others.
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GH: See other's posts to the list. GH's summary.

Gregg will send out side-by-side DAS/1 and DAS/2 UML models (pictures and/or
model files).
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GH: See 29-oct-08 post to the list for these.
JW: Could get technical, esp. for alignments.
GH: Teleconf can be more efficient than email, though face-to-face is best.
AJ: Can put it at the end of the discussion.

Gregg: write proposed changes to sources document more formally.
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(Pending)

UK folks: Continued Das integration work (spec review)
-------------------------------------------------------

JW: No comments posted. Planning to try RNG instead of XSD. Good
suggestion. Working on validation. Will post these next week.

GH: There is a nice RNC mode in emacs, and in-line realtime validator that
will
validate against a document.

Anyone interested in contributing: look at links from Andy/Jonathan on how
das1 is changing.
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GH: Regarding DAS changes document, I can start editing with how it
changes for DAS/2. But could get long.
JW: That's fine.

GH: Regarding plans to deprecate the DSN: I like this, but will
require changes to the sources document to fully deprecate
it. Example: Map masters not reflected in the registry.
JW: OK. We're open to any changes.

Steve: wikify the HTML docs.
-------------------------------

SC: Wikified as of last night (10/29). Left-hand nav of biodas.org
link has been updated and DAS/2 page updated to point to wikified spec
at http://www.biodas.org/wiki/DAS/2/Spec

AL: Concerned that it is not noted as "under development". There
should be a fixed version of the spec and a draft version so that
people know what they're using.

SC: Can flag the wikified spec as "evolving" and have pages be
DAS/2.1. The HTML version of the spec can be flagged as "frozen".
Will post a link to the list when ready.

All: Teleconf in two weeks, same time, but need better phone line!
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New number for this meeting is not long-term (GH is paying for).
GH: Can probably use Suzi's long-term. Her laptop is offline
currently, but we should be able to get the info before next meeting.

New Topics
============

JW: DAS workshop at Hinxton on 9-11 March. Tutorial day1, das
project talks das2, hackathon day3, more programming work, das1-2
merging, etc. Not tied to other meeting. Sponsored by BioSapiens.

GH: Love to attend, but need funding. Would like to host a workshop on
West coast at some point. Prob best time 6 mos after UK. Hackathon-style.

SC: Can you post it to biodas.org current events?

AJ/JW: It's not yet been announced. Will do eventually.

AL: Working on changes to das server to support Arabidopsis data and
also some IGB mods. Will test before posting. Hosting of bioviz.org.

Plan to host Java Web start for IGB on bioviz.org, based on SVN
codebase in SF.  

JN: The Affy links to launch IGB on the SF page are broken.

[A] Steve: Fix Affy IGB launching links on SF page.

SC: You will need a code signing certificate because IGB needs to
write to the local disk. Affy's cert is expiring in December, but
don't need to renew if yours will be ready by then. What's
your time frame?

JN: Can look into getting something preliminary posted soon.

GH: Need a release that can support the translational proxy. Will talk
about this with AL offline.

Topic: Gregg's translational proxy
====================================

GH: Has anyone looked at this yet?
AJ: Have looked at code, not XML. Will check it out.

GH: What it is doing: Das ID -> URI conversion. Hit some issues where
some das IDs aren't really URI or URI refs. Using XML base features of
das2, using a shorthand version of the URI (XML base space provides
way to resolve them into full URIs).

Other stuff: tell if a field (e.g., phase or score) is null or not
available, will strip those out to avoid overhead of empty
elements. When there are values which aren't in DAS/2 protocol,
it converts into das/2 properties with "DAS1:" prefix. Seems to work
well. Looked at some examples, none of which had non-nulls, so you
can't see this. Will post some examples to illustrate.

Other thing (trying to do): Mapmaster in DSN not listed in
registry. Lots of things in registry w/ no pointer to entry points, but
have a shared coord system.

AJ: Don't worry about DSN command now. Every coord sys will have a ref
server that will implement entry points and sequence.
GH: Good. Would like to change this in the doc.
GH: Doing a transitivity thing based on entries with entry points but
not coord systems, or vice versa. With proxy system you can infer
things over multiple sources.

Other things; Proxy taking das1 registry sources --> das2 sources
document, leaves all das1 capabilities in tact, so it has both das1
and das2 (a hybrid).

GH: Test deployment is sitting on Amazon cloud in Genomancer. Want it
hosted on Sanger/EBI closer to the registry, will help for
efficiency. 
JW: Can look at putting it up there. Need to look at the proxy.

Topic: Gregg's Trellis/Vine/Ivy project
===========================================

GH: Trellis project (the foundation for das1->2 proxy). Trellis is a
modular das2 server/servlet framework. Take das2 data model, plug it into
trellis to get a functional das2 server. Plan to move UCSC das2 server
to be a plugin for trellis. Framework deals with query parsing and
generating xml. Plugin is just dealing with data models.

Also das2->2 proxy as well. for das2 server that don't implement alt
content format. A proxy might be able to serve those up.  Vine module
has full das2 client library. To do a full proxy, you need a client.

Ivy: This is the das1 part of the das1->2 proxy.

Pleased with this as a framework for further development. All future das2
work will be on trellis framework. This had a larger scope than
anticipated, hence the extra time to develop.

SC: Any docs?
GH: None, other than UML.

SC: So trellis is framework. Ivy, Vine are plugins?

Noting from Gregg's DAS list post:
  * Trellis: DAS/2 server framework
  * Vine: DAS/2 proxy plugin
  * Ivy: DAS/1 proxy plugin

GH: There's a plugin API in the Trellis servlet specifying that plugin
specifies the sources capability data model, the rest of data model is
under sources. Vine=DAS2 proxy. Much impl can be obtained from that
(e.g., has stubby getters and setters). Plugin dev focus is on
capability API. 

Action Item Summary:
========================

Old action items:
-----------------

[A] Suzi: Decide Ian or Suzi is PI on grant. Issue reciprocal letters of
collab. (16-oct-08)

[A] Suzi: Summation of authentication pros and cons. Review descriptions,
make a decision. (16-oct-08)

New action items:
-----------------

[A] All: Next teleconf in two weeks: 13-Nov-08

[A] All: Anyone that has items they want discussed, send to Gregg.

[A] All: Review Gregg's DAS UML modeling, post any comments to list.

[A] All: Review Gregg's DAS1->DAS2 proxy work (Trellis/Ivy/Vine), post any
comments to list.

[A] AJ: Post info about March '09 Hinxton DAS workshop to
biodas.org/current_events

[A] AJ: Continue checking out Gregg's DAS1->DAS2 proxy, esp. the XML.

[A] GH: Send out action and agenda items well in advance of teleconf.

[A] GH: Add auth and security on the agenda so interested folks can call in.

[A] GH: Solicit feedback about security/auth from interested parties.

[A] GH: Contribute to the DAS changes document re: DAS/2, sources &
deprecating DSN.

[A] GH: Get new teleconf number from Suzi; post to list with agenda.

[A] JN: Post preliminary java web start IGB release on bioviz.org

[A] SC: Merge DAS2 subscribers to DAS list. Redirect DAS2 posts to DAS list.

[A] SC: Consider making DAS list auto reject posts from non-subsribers.

[A] SC: Add Andy J and Jonathan W as admins to the DAS mailing list.

[A] SC: Change 2 -> 2.1 and say it is "evolving"; declare the HTML spec as
"frozen"

[A] SC: Send link to the 2.1 wiki spec to list.

[A] SC: Fix Affy IGB launching links on SF page.

[A] SC: Update biodas.org community portal page with new teleconf number.

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Minutes are committed to the biodas.org CVS repository under
biodas/das/das2/notes/

$Id: das2-teleconference-2008-10-30.txt,v 1.4 2008/10/30 18:55:42 sac Exp $