[DAS2] Notes from the weekly DAS/2 teleconference, 25 Sep 2006

[Steve Chervitz]

Notes from the weekly DAS/2 teleconference, 25 Sep 2006

$Id: das2-teleconf-2006-09-25.txt,v 1.2 2006/09/25 17:38:57 sac Exp $

Note taker: Steve Chervitz

Attendees: 
  Affy: Steve Chervitz, Ed Erwin, Gregg Helt
  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. 


Agenda
-------

* Spec issues
* Grant status
* Status reports

Topic: Spec issues
------------------

aday: what is the status of the currently posted spec w/r/t fasta
format, seq segments? The fasta description in the spec seems not up
to date. 
gh: as I recall from the last code sprint (aug 14-18 2006), we had
decided to return a das2 segments document in which you could specify
fasta as an available format for receiving seq data.
sc: that's my recollection too.

[A] andrew will work more on keeping the online spec up to date.

Topic: Grant status
-------------------

gh: We have received official word of approval of $250K for extending
funding from now thru May 2007. Allen and Ed will be at same amt, steve
down a bit - based on current billing, gregg up 40-50%. This will
allow me to put more focus on grant. Funding will also be put towards
equipment improvements for affy das/2 server on our colo.

andrew will start a full time job in 2007, will ramp up till end of
year. hoping he can get a lot of the spec issues put to rest before he
goes. probably it will be me (gregg) taking up the spec when he
leaves, and hoping I won't have much to do on the spec docs.

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

gh: have worked on the das/2 budget last 2 weeks. now should be able
to get back to coding. has allen and brian received their
reimbursements from code sprint?
aday: brian got his, not me yet.
gh: should get yours soon.

ee: putting out a new release of igb this week. minor release.

sc: helped straighted out file/dir permissions at biodas.org, lincoln
was posting an update the to Bio::Das section on the biodas.org ftp
site.
gh: his new das/2 client in perl? he's been working on that.
sc: not sure, possibly.
sc: also talked with gregg regarding my time commitment for the das/2
extension period. will be able to devote a solid block of time (~4wks)
sometime in Dec or Jan.

aday: diagraming to get the current state of the spec. getting ready
to do major server side rewrite, implemented block caching strategy,
to allow same data source to do reads and writes. going with custom
caching rather than apache mod proxy, gives us more control of operations.

Performance improvements I did on the chado db can then be removed
since everything will be cached. working on uml diags.

gh: are you doing from scratch caching?
aday: we have a mvc app. model layer talks to db,
inherits from abstract db. that will stay the same. handles conversion
of query string into sql. maybe trim it down and simplify based on
spec cruft losses. 
for view and controller components, we use templates to generate xml.
that will stay same, will use the catalyst web frame work, much like
ruby on rails, executable scripts that generate code for v and c
layers. will replace the current hand code with the catalyst generated
stuff.  
sc: so this is like Ruby on Rails for perl?
aday: yes

aday: question on hw budget on this current round of funding?
gh: yes. we originally discussed more hw for ucla or cshl. now looking more
doubtful. would like to address towards end of year or jan.
based on prev estimates, we never spend as much as budgetted for. if
more left over, we can look into putting more hw. the affy hw is a
sure thing. is need critical?
aday: there is pressure on our hw to do upgrades, used by rest of lab
as well now. maybe $5K would do it. dual or quad 4.
gh: do able sooner rather than later. send some figures...

[A] Allen will send gregg estimates on needed das-related hw upgrades at
ucla.