[Gusdev-gusdev] Summary of last conference call

[Chris S. <sto...@SN...>]

Thanks to Jonathan Crabtree who generated this the day of the call. 
Sorry it took so long to distribute this.
At the end are action items for which there has already been some 
action. I have added notes to that effect.

Cheers, and best wishes for your meeting next week!
Chris

Conference call on September 11, 2002

***Attending:

CBIL: Jonathan Crabtree, Joan Mazzarelli, Deborah Pinney, Jonathan Schug,
       Yongchang Gan, Chris Stoeckert, Steve Fischer
PSU:  Marie-Adele Rajandream, Arnaud Kerhornou, Christiane Hertz-Fowler,
       Paul Mooney, Adrian Tivey, Matt Berriman (sorry if I missed anyone;
       I forgot that I was supposed to be taking notes at this point - JC)

***Loading data for orthologous groups
Marie-Adele raised the issue of loading data on orthologous groups for
the PSU databases, and specifically our earlier promise to make Li's
code for doing this available by September.  Nobody present had talked
to Li recently, so we promised to follow up with her (see action item
1.)  We confirmed that the information isn't needed immediately (i.e.,
for the Woods Hole meeting on the 22nd), but that the PSU group would
like to have it sooner rather than later.

***GUS 3.0 migration
As part of the above discussion the question of the CBIL GUS 3.0
migration was raised.  This is also something that we had earlier said
we would have finished by September.  In Chris's absence Jonathan C.
made the (perhaps controversial) statement that although it was still
a high priority he suspected that the upcoming PlasmoDB release (in the
first week of October) would quite likely delay substantial progress
on the migration until then.  That is, the decision to use GUSdev in both
the next PlasmoDB release and also the GeneDB demo at Woods Hole has
diverted development effort to GUSdev that could otherwise have been
applied to the GUS 3.0 migration.

***Schema changes
Arnaud raised the issue of schema changes needed in the short term
(by next week) for RNAFeatures.  We agreed that once consensus had been
reached on a proposed schema change on the GUSdev mailing list we
would implement it ASAP and update the create schema scripts in the
CVS repository.  We asked Arnaud to send/reconfirm his request by
e-mail and promised to make the necessary changes forthwith (action
items 2 and 3).

***CVS repository and new GUS/GUSdev home page
The question of a CVS web interface was raised again but since the
Sanger admins have been busy installing new hardware, no changes have
been made to the existing CVS servers.  With respect to having a
dedicated GUSdev home page, it was resolved that Steve F. would set
something up on one of the CBIL web servers, using the gusdev.org
domain that we'd acquired previously (action item 4).  The new home
page will provide a friendly face to the GUS project and will link to
other sites (e.g., Sourceforge or Sanger CVS) as necessary.  If
possible the site will be set up in such a way that both groups are
able to contribute content.

***Woods Hole Requirements (GUSdev distribution and installation)
Paul reported that the PSU's Oracle server was in the process of being
moved, and so he hadn't yet had a chance to try generating the Perl
object layer from the GUSdev tar file generated by Jonathan C.  He
also stated that he was collecting a list of problems with the
installation process (mostly minor so far) that he would e-mail to
Jonathan C.  when complete (action item 5).  Jonathan C. said that he
would check the tar file into the Sourceforge CVS repository (under
/scratch) after writing a short summary to put in the README file
(action item 6).

***Representing phenotypes
Chris S. pointed out that the notion of phenotype implied by Christiane's
e-mail was somewhat wider in scope than what we'd originally had in
mind.  That is, the RNAi example given includes not only the observed
phenotype (e.g., slow growth) but also the (RNAi-based) assay used to
elicit that phenotype from a hapless collection of Trypanosomes.  The
conclusion was that we would definitely be able to come up with a set
of tables to represent everything, but that it might take a bit of
discussion.  In the intermediate term it was agreed that the PSU
annotators would be able to store this type of information in free
text fields, specifically entries in the "Note" table, which is able
to link to any NAFeature.  Arnaud also suggested that we look at the
new Flybase schema (in which they are also making a transition from
free text phenotype representations to greater use of controlled
vocabularies), and said that he would send around a link (action item 7).

***Biojava/JSP development for GUS 3.0 interfaces
Biojava was mentioned and Jonathan C. said that he (and Dave Barkan,
the programmer working on the project) would be evaluating whether it
could be used productively in CBIL's new annotator interface.  Jonathan
promised to send periodic updates to the GUSdev mailing list (on the
status of the CBIL annotator interface) to solicit feedback, and find
out if there are any areas of development where we could collaborate
(action item 8.)
Adrian had earlier brought up the question of developing the JSP
infrastructure for the GUS 3.0 web interfaces.  He is going to come up
with a list of requirements and we are going to start brainstorming
about the design over the mailing list (action item 9).

***Meetings
There was some discussion of who would be at what meetings; Chris
S. and Trish Whetzel are the only ones from CBIL who will be attending
the November meeting at Sanger.  Matt also asked about the upcoming
TIGR ontology meeting (action item 10); currently nobody from either
group plans to attend.

***ACTION ITEMS:
  1. Make Li's poster and code available [Li]
Li's poster is available at  
http://www.cbil.upenn.edu/downloads/GUS/documentation/ISMB2002/.
Li's code for loading ortholog tables in gusdev is at: 
http://www.cbil.upenn.edu/downloads/GUS/releases/2.0.1/source-code/
  2. E-mail schema changes [Arnaud]
  3. Apply schema changes, update scripts/CVS [Jonathan C.]
  4. Set up stunning new GUSdev web site on gusdev.org [Steve F.]
See http://www.gusdb.org!
  5. Collect list of problems with GUSdev source code tar file and
     e-mail to Jonathan C./GUSdev mailing list [Paul]
Sent to Jonathan C.
  6. Check GUSdev tar files (schema scripts + Perl/Servlet source code)
     into the Sourceforge CVS repository under /scratch [Jonathan C.]
  7. Send around pointer to new Flybase schema [Arnaud]
  8. Communicate status/design of annotator's interfaces on a periodic
     basis, maintain dialog over possible uses of biojava, collaboration
     on interfaces and/or implementation [Jonathan C., all developers]
  9. Compile user interface "wish list" and send it out as an opening
     salvo in a discussion on the future JSP architecture [Adrian]
10. Send around pointer to TIGR ontology meeting [Matt]
Sent to Chris.