[DAS2] DAS/2 weekly meeting notes
Steve_Chervitz at affymetrix.com
Sat Oct 22 00:48:57 UTC 2005
Notes from the weekly DAS/2 teleconference, 21 Oct 2005.
$Id: das2-teleconf-2005-10-20.txt,v 1.1 2005/10/21 23:55:05 sac Exp $
* Gregg and Lincoln hashed out some details regarding specific aims
for the DAS/2 continuation grant, refining these aims:
- Client enhancements
+ includes client-side caching
- Spec enhancements
+ caching (IF_MODIFIED_SINCE support)
+ dealing with lengthy server operations
+ extensions to stylesheet capabilities
+ embedding arbitrary snippets of XML (e.g., RDF)
- IGB-Apollo interactions
+ Gregg has been doing some background research on HTTP and
* Greg plans to have a draft ready to circulate for review by the
participating organizations by Tues next week (10/25).
* DAS/2 meeting at CSHL Genome Informatics meeting:
- Planned for 10/28 evening (7:30pm EDT) in Lincoln's office
- Teleconf will be available
* Proposal to move the weekly DAS/2 meeting to 9:00am PDT/PST Thursday
so that UK folks can participate
- Folks will check schedules to see if this works
- Chime in if it doesn't work for you
* Completed treeview of DAS/2 sources in IGB. See his recent post with
GUI snapshot. This will be included by default in the next
IGB release next week, to coincide with the CSHL GI meeting.
* Invited to talk at CSHL GI meeting on genome viz. Good opportunity
to present IGB. May accept the invitation if it's later during the
* Is making an effort to respond to questions on the DAS/2 list.
* IGB release planned for next week, coinciding with CSHL GI meeting.
- Lots of new additions (DAS/2 support, new GUI preferences
setting). Might be a 4.0 release.
- Access via Java Web Start
- Users will be able to launch previous version of IGB, if they
have problems with the new version.
- Ann Loraine puts in a strong plug for JWS-based application
launching. It's just so convenient, even for someone who is
comfortable building and running java code with command-line tools
(but doesn't always have time to do so these days).
- Gregg would like to set up an auto-build system for IGB code on
SourceForge (or open-bio.org, if SF doesn't support this). This
would allow users to download a pre-built jar. A JWS system could
then be built on top of this if we want.
* Lots of IGB commits last week.
- Can now set persistent preferences via GUI rather than pref file
(bg colors, feature colors, number of levels of a given tier,
show/hide prefs, etc.). Much nicer user experience.
- No documentation yet.
- Gregg adds: Deb Coulton (sp?) is now revising the IGB user
guide. Targeting end of Nov for release.
* Working on improving the DAS/2 spec, resolving bugzilla issues,
consistent wording, etc.
- See http://biodas.org/documents/das2/das2_get.html
- Be sure to force your browser to reload the page daily to make
sure you have the latest version.
- Will post notable changes to the DAS/2 list.
- Will post any issues requiring broader discussion to list before
- Gregg adds: See his response to Andreas on the list regarding how
to deal with server agreement on what sequence coordinate system
is being used. Do folks agree with Gregg's proposal?
* Bug fixes on biopackages.net DAS/2 server
- A DAS2XML parser would help catch bugs in advance. Will ask
Andrew about setting this up.
* Discussed performance issues.
- Feature request is as fast as it's going to get now (in terms of
- Has a SQUID proxy set up to help with relatively static data, but
you must configure your client to use it.
(also ss Allen's post on 10/21 regarding aache mod_cache module).
- Gregg adds: Would like to get support in spec for 'if modified
- Gregg: What about using a different schema underneath, such as
GFF-db as used by gbrowse which is quite fast?
- Allen: It's not fast for large segments. The DAS/2 server uses a
chado schema with feature indexing optimizations by Allen. It's
performance improves for big queries, but degrades for small
queries. So the DAS/2 server's response is more flat over a range
of query sizes relative to gbrowse.
Possibly could improve the DAS/2 server by upgrading from
Postgres 7.4 to 8.0, which has improvements on left joins.
- Lincoln: How could gbrowse performance be improved?
- Allen: Via partial indexing. Should improve for queries covering
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