[Gusdev-gusdev] FW: conference call summary

[Marie-Adele R. <ma...@sa...>]

Chris,

No changes from us.  It is fine.  I have forwarded it to the gusdev-mail
list.

Marie-Adele

-----Original Message-----
From: Chris Stoeckert [mailto:sto...@SN...]
Sent: 11 September 2002 20:48
To: cra...@SN...
Cc: Marie Adele
Subject: Re: Draft of conference call summary


Jonathan,
Thanks. Very comprehensive and certainly more amusing than my summaries.
I am forwarding this to Marie-Adele.

Marie-Adele,
Please forward this to the gusdev-mail list with any additions or edits
that you feel are necessary.
Thanks,
Chris

On Wednesday, September 11, 2002, at 11:55 AM,
cra...@SN... wrote:

>
> Chris-
>
> A summary is attached; I think that you only missed the first 1 or 2
> items
> on the list.
>
> Jonathan
>
> --
> Jonathan Crabtree
> Center for Bioinformatics, University of Pennsylvania
> 1406 Blockley Hall, 423 Guardian Drive Philadelphia, PA 19104-6021
> 215-573-3115
>
> 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, Christopher Peacock
>       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]
>  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.]
>  5. Collect list of problems with GUSdev source code tar file and
>     e-mail to Jonathan C./GUSdev mailing list [Paul]
>  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]
>