October 2005 GMOD Meeting
Generic Model Organism Database Construction Set
Contents
Meeting 7
Thursday, October 27, 2005 Gerry Conference Room, Marks Building, CSHL
Agenda
9:10am
Introductions
Scott Cain, GMOD coordinator
9:30
GMOD/chado 0.003 and roadmap, including:
- improvements for next release
- standardizing chado use across orgs
- upgrade paths (script to modify data and schema?)
- other topics that should be discussed during this meeting
10:30
Break
10:45
Top ten things a MOD provides
more on the road map; how Chado, GBrowse, Turnkey and Apollo fit in and
where the holes are
12:00
Lunch
1:30
architecture working
group:
Review and revisit what we have done
2:00
Testing Recommendations
2:45
Break
3:00
Java O/R recommendation
3:30
Discussion: other topics, either architecture or other software issues
Friday, October 28, 2005 DIFFERENT ROOM: Plimpton Conference Room, Beckman Building, CSHL
| 9:10 |
Common URLs and common gene page |
| 10:30 |
Break |
| 12:00 |
Lunch |
| 1:30 |
Revisiting the developer's guide; preparing a software
package for release |
| 2:00 |
Software demos, coffee
|
Meeting Report
Meeting report for October, 2005 GMOD meeting. This is an outline by
Scott Cain.
Topics covered:
- Current state of gmod/chado release, movement towards 0.1 release
- Discussed ‘MOD Top Ten list’
- Mike Cherry proposed operating a MOD ‘co-location’ facility with all
GMOD tools. The may be greatly facilitated by the software packaging
work done by Allen Day and Brian O’Connor with
biopackages.net.
- Some discussion of using a content management tool like
Drupal to handle some of the page display tasks
for a MOD and use turnkey only as a tool to
access and display
chado related
data.
- Architecture
- Testing recommendations
- Volunteers to examine Java ORMs Hibernate and
iBatis
- How to get various chado instances to conform to a standard method
of encoding data? Documentation: Joshua (TIGR) volunteered to
document how TIGR is using chado to encode data and make it public
as a first step in a collaborative effort among current users of
chado (including TIGR,
FlyBase, and GMOD
developers).
- www.gmod.org
- In the evening of the first day, Allen Day, Brian O’Connor and Scott
Cain created a prototype website with the purpose of improving the
function of the site. It is based on an open source content
management software package that will facilitate collaborative
documentation projects, such as the chado usage project discussed
earlier that day.
- Common gene page. Since this group does not represent the target
users, we did not feel that we would make much headway in establishing
a standard. However, it was noted that the data collected by GO for
several organisms contains much of the data that would be needed for a
simple gene page. It was decided that Scott Cain would create a gene
page using this data and present it at the biocurators meeting in
December
- Software developer’s guide and software release recommendations
- stuff to do
- Scott: build sample gene page from GO gene data (or talk Chris into
doing it) hopefully to present to biocurator list in December
- Migrate website to facilitate documentation improvements
- key to improving standards for chado usage
- follow up on getting/comparing data dumps for different chado
implementations
- Talk to lincoln about identifying a journal for publication
- demos
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